The invention relates to three-dimensional Paul RF ion traps with high efficiency for the collection of analyte ions provided for subsequent reactions, especially for monomolecular reactions or reactions with reactants, preferably for reactions between positive analyte ions and negative reactant ions.
As is well known, three-dimensional Paul RF ion traps consist of at least one ring and two end cap electrodes, and operate with an RF voltage between ring and end cap electrodes. In most cases, only a single phase of this voltage is used, applied to the ring electrode. If the electrodes are designed as ideal hyperboloids of revolution, the strength of the RF field increases linearly from the center outwards in all spatial directions, hence the term “three-dimensional”. An inhomogeneous RF field is therefore generated in the interior. Any inhomogeneous electric RF field acts on ions in a way which can be described by a so-called “pseudopotential”. The pseudopotential increases quadratically in a three-dimensional RF ion trap in all spatial directions and has a minimum in the center of the ion trap; it drives the ions of both polarities from all spatial directions into the center of the ion trap and thus makes them oscillate through or around the center. If the electrodes are of the ideal shape, the pseudopotential is harmonic; it makes the ions oscillate harmonically. Harmonic oscillation is characterized by the fact that its oscillation frequency always remains the same, regardless of the oscillation amplitude.
If the ion trap is filled with a collision or damping gas at a pressure between 0.001 and 1 Pascal, the oscillations of ions introduced from outside through apertures in the end cap electrodes are damped so that the ions finally collect in a small cloud in the center of the ion trap. The size of the cloud is determined by the centripetal force of the pseudopotential field in the ion trap and the centrifugal force caused by the Coulomb repulsion between the ions. Since the pseudopotential acts on positive and negative ions in the same way, ions of both polarities can be captured. In particular, it is also possible to capture both ion species simultaneously or consecutively so that they react with each other in the damped ion cloud.
Such reactions between positive and negative ions are analytically of great interest. It is thus possible to use specific types of negative reactant ions to cleave multiply positively charged peptide or protein ions by a transfer of an electron (“ETD”=electron transfer dissociation), as described, for example, in the patent application publications DE 10 2005 004 342 A1 (R. Hartmer and A. Brekenfeld) and US 2005/0199804 A1 (D. F. Hunt et al.). The multiply charged positive peptide or protein ions which are analyzed with this method form the “analyte ions” introduced above. The electron-induced dissociation of the analyte ions is complementary to the collision-induced dissociation (CID) because, firstly, it cleaves at different points of the amino acid chain and, secondly, it does not split off the side chains of the post-translational modifications (PTM) during fragmentation, as happens with collision-induced dissociation.
On the other hand, reactions between multiply positively charged analyte ions and certain types of negatively charged ions can also be used to reduce the number of charges on each of the positive analyte ions (“PTR”=proton transfer reactions, also called “charge stripping”). Charge stripping makes it possible to convert very heavy, highly charged analyte ions into ions whose isotope patterns can be resolved in the mass spectrometer. The analyte ions can be, for instance, converted right down to singly-charged ions in order to reduce the complexity of mixtures of many heavy, highly charged analyte ions.
In three-dimensional ion traps, ions can also react with neutral particles if these are introduced into the ion trap. This makes it possible to generate derivatizations, for example, or to label by using heavy isotopes of an element, such as by replacing hydrogen with deuterium. Also, of particular significance is electron transfer by highly excited neutral particles, which leads to similar fragmentations as electron transfer by negative ions. Such highly excited neutral particles can be generated in a so-called “FAB source” (FAB=fast atom bombardment), which generates a well-directed, fine beam of highly excited atoms, for example highly excited helium atoms. This beam can be directed very effectively through a hole in the ring electrode at the small cloud of analyte ions which forms in a three-dimensional ion trap. The elongated thread-like cloud of analyte ions which builds up in a linear ion trap does not lend itself easily to the use of a conventional FAB source for the fragmentation unless the beam of neutral particles can be directed along the axis into this cloud.
So-called “unimolecular reactions” without reactant substance molecules or ions are also possible, as occur with bombardment with sufficient quantities of infrared photons (IRMPD=infrared multiple photon dissociation), for example. This type of bombardment can also be carried out particularly well in three-dimensional ion traps because of the formation of a small spherical cloud.
Three-dimensional RF ion traps themselves can also be used as mass analyzers for the product ions created. They then have to very precisely maintain a certain shape of electrode to enable a precisely resonant excitation, especially for a good mass-resolved ejection of the ions for measurement in a mass spectrum. The precise form is necessary to ensure that, by means of a good harmonic pseudopotential field, the excitation frequencies of the oscillating ions during resonant excitation are kept constant and independent of the oscillation amplitude. The electrodes must be designed so as to generate a very well-formed quadrupole field in the interior. In some quadrupole mass spectrometers, however, small amounts of higher multipole fields are also very precisely superimposed on the quadrupole field. Such willfully generating deviations from the pure quadrupole field can, on the one hand, introduce non-linear, very strong and sharp resonance conditions and, on the other hand, keep the ions in resonance while a mass scan is in progress.
However, this precise form, which consists primarily of smooth-surfaced ring and end cap electrodes in the precise shape of a hyperboloid of revolution, means that the capture of the ions introduced from the outside is limited to some 5% to 10% of the analyte or reactant ions which are fed in. This limitation is the biggest disadvantage of the high-precision hyperboloid of revolution RF ion traps, which have been used exclusively until now in commercially produced ion trap mass spectrometers. Frequently, the analyte ions are only present in very small quantities in a sample. Consequently, the detection sensitivity of the ion trap mass spectrometers, which is very important in bioanalysis, is reduced.
The success rate for ion capture in so-called “linear multipole ion traps”, which comprise four or more pole rods, is much higher. In a linear ion trap, the ions are driven radially toward the axis by the pseudopotential; they gather in an elongated ion cloud along the axis. The linear ion trap is also often called “two-dimensional” because the pseudopotential changes only in two spatial directions and remains constant in the third spatial direction, the axis of the linear ion trap. The ions are introduced axially with low kinetic energy and can easily be captured in the elongated ion trap by a collision gas if the mean free path in the collision gas is kept sufficiently short by a suitable pressure. If the ions are introduced precisely centrally in the axial direction, they do not come up against a decelerating RF field in any phase; slightly outside the axis there are weak fields which have the effect of focusing the ions toward the axis. Ions can therefore be injected with low kinetic energy and captured with a high yield.
Linear ion traps must, however, be closed off at both ends by repulsive potentials in order to prevent the ions from simply escaping. DC potential barriers at apertured diaphragms are generally used for this, but it is then only possible to store ions of a single polarity, i.e. either positive ions or negative ions. It is also possible, in principle, to generate pseudopotential barriers at both ends, but this is much more difficult than producing the boundary with DC potential barriers, and is therefore hardly ever used in practice. Unless special mechanical and electronic measures have been taken, linear ion traps therefore have limited use for reactions between positive and negative ions. Moreover, the cooled ions are not located in an almost spherical cloud, but instead form an elongated cloud which stretches along the axis of the linear ion trap.
If reactions between positive and negative ions are to be brought about in such linear ion traps, the clouds of positive analyte ions and negative reactant ions are sometimes collected in separate sections of a segmented linear ion trap, called “pre filter” and “post filter”, and are then fed to a thorough mixing in the center part of the linear ion trap by a special configuration of the axis potentials. This method is explained in great detail in the publication of patent application US 2005/0199804 A1 (D. F. Hunt et al.), already cited above.
This method has disadvantages, however. If a fragmentation by electron transfer is carried out, for example, the heads of the two ion clouds penetrate each other initially, and their ions react with each other. With further penetration, the positive fragment ions formed in the cloud heads can react further in an undesirable way with subsequent negative reactant ions, and some of them can be completely neutralized before the analyte ions in the tail of the cloud have even come into contact with the first reactant ions. This disadvantage does not occur in three-dimensional RF ion traps because the reactions occur in a very homogeneous way.